Improving bioinformatics software quality through teamwork.

Autor: Ferenc K; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo 0318, Norway., Rauluseviciute I; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo 0318, Norway., Hovan L; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo 0318, Norway., Kumar V; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo 0318, Norway., Kuijjer ML; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo 0318, Norway., Mathelier A; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo 0318, Norway.; Department of Medical Genetics, Institute of Clinical Medicine, Oslo University Hospital and University of Oslo, Oslo 0450, Norway.; Department of Pharmacy, University of Oslo, Oslo 0371, Norway.

Publikováno v: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Nov 01; Vol. 40 (11).

Biological Sample Collection to Advance Research and Treatment: A Fight Osteosarcoma Through European Research and Euro Ewing Consortium Statement.

Autor: Green D; Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich, United Kingdom., van Ewijk R; Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands., Tirtei E; Pediatric Oncology, Regina Margherita Children's Hospital, Turin, Italy.; Department of Public Health and Pediatrics, University of Turin, Turin, Italy., Andreou D; Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria., Baecklund F; Pediatric Oncology Unit, Karolinska University Hospital, Stockholm, Sweden., Baumhoer D; Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland., Bielack SS; Center for Pediatric, Adolescent and Women's Medicine, Klinikum Stuttgart-Olgahospital, Stuttgart Cancer Centre, Stuttgart, Germany., Botchu R; Department of Musculoskeletal Radiology, Royal Orthopaedic Hospital NHS Foundation Trust, Birmingham, United Kingdom., Boye K; Department of Oncology, Oslo University Hospital, Oslo, Norway., Brennan B; Paediatric Oncology, Royal Manchester Children's Hospital, Central Manchester University Hospital NHS Foundation Trust, Manchester, United Kingdom., Capra M; Haematology/Oncology, Children's Health Ireland at Crumlin, Dublin, Ireland., Cottone L; Department of Pathology, UCL Cancer Institute, University College London, London, United Kingdom., Dirksen U; Pediatrics III, West German Cancer Center, University Hospital Essen, German Cancer Consortium (DKTK) Site Essen, Cancer Research Center (NCT) Cologne-Essen, University of Duisburg-Essen, Essen, Germany., Fagioli F; Pediatric Oncology, Regina Margherita Children's Hospital, Turin, Italy.; Department of Public Health and Pediatrics, University of Turin, Turin, Italy., Fernandez N; Patient and Parent Advocacy Group, FOSTER, Washington, District of Columbia., Flanagan AM; Department of Pathology, UCL Cancer Institute, University College London, London, United Kingdom.; Histopathology, The Royal National Orthopaedic Hospital NHS Trust, Stanmore, United Kingdom., Gambarotti M; Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy., Gaspar N; Department of Oncology for Child and Adolescent, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.; U1015, Université Paris-Saclay, Villejuif, France., Gelderblom H; Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands., Gerrand C; Orthopaedic Oncology, The Royal National Orthopaedic Hospital NHS Trust, Stanmore, United Kingdom., Gomez-Mascard A; Department of Pathology, Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France.; EQ ONCOSARC, CRCT Inserm/UT3, ERL CNRS, Toulouse, France., Hardes J; Tumour Orthopaedics, University Hospital Essen, German Cancer Consortium (DKTK) Site Essen, Cancer Research Center (NCT) Cologne-Essen, University of Duisburg-Essen, Essen, Germany., Hecker-Nolting S; Center for Pediatric, Adolescent and Women's Medicine, Klinikum Stuttgart-Olgahospital, Stuttgart Cancer Centre, Stuttgart, Germany., Kabickova E; Paediatric Haematology and Oncology, University Hospital Motol, Prague, Czech Republic., Kager L; Pediatrics, St Anna Children's Hospital, Medical University Vienna, Vienna, Austria.; St Anna Children's Cancer Research Institute, Vienna, Austria., Kanerva J; Hematology-Oncology and Stem Cell Transplantation, HUS Helsinki University Hospital, New Children's Hospital, Helsinki, Finland., Kester LA; Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands., Kuijjer ML; Computational Biology and Systems Medicine Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway.; Pathology, Leiden University Medical Center, Leiden, the Netherlands.; Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, the Netherlands., Laurence V; Department of Medical Oncology, Institut Curie, Paris, France., Lervat C; Department of Pediatrics and AYA Oncology, Centre Oscar Lambret, Lille, France., Marchais A; Department of Oncology for Child and Adolescent, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France., Marec-Berard P; Institute of Hematology and Pediatric Oncology, Léon Bérard Center, Lyon, France., Mendes C; Portuguese Institute of Oncology of Lisbon, Lisbon, Portugal., Merks JHM; Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands.; Division of Imaging and Oncology, University Medical Center Utrecht, Utrecht, the Netherlands., Ory B; School of Medicine, Nantes Université, Nantes, France., Palmerini E; Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Orthopedico Rizzoli, Bologna, Italy., Pantziarka P; Patient and Parent Advocacy Group, FOSTER, Washington, District of Columbia.; Anticancer Fund, Meise, Belgium.; The George Pantziarka TP53 Trust, London, United Kingdom., Papakonstantinou E; Pediatric Hematology-Oncology, Ippokratio General Hospital of Thessaloniki, Thessaloniki, Greece., Piperno-Neumann S; Department of Pediatrics and AYA Oncology, Centre Oscar Lambret, Lille, France., Raciborska A; Oncology and Surgical Oncology for Children and Youth, Institute of Mother and Child, Warsaw, Poland., Roundhill EA; Children's Cancer Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom., Rutkauskaite V; Center for Pediatric Oncology and Hematology, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania., Safwat A; The Danish Centre for Particle Therapy, Aarhus University Hospital, Aarhus, Denmark., Scotlandi K; Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy., Staals EL; Orthopaedics and Trauma, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy., Strauss SJ; Department of Oncology, University College London Hospitals NHS Foundation Trust, UCL Cancer Institute, London, United Kingdom., Surdez D; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland., Sys GML; Department of Orthopaedic Surgery and Traumatology, Ghent University Hospital, Belgium., Tabone MD; Department of Hematology and Oncology, A. Trousseau Hospital, Sorbonne University, APHP, Paris, France., Toulmonde M; Department of Medical Oncology, Institut Bergonié, Bordeaux, France., Valverde C; Medical Oncology, Vall d'Hebron University Hospital, Barcelona, Spain., van de Sande MAJ; Orthopaedic Oncology, Leiden University Medical Centre, Leiden, the Netherlands., Wörtler K; Musculoskeletal Radiology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany., Campbell-Hewson Q; Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom., McCabe MG; Division of Cancer Sciences, School of Medical Sciences, The University of Manchester, Manchester, United Kingdom.; The Christie NHS Foundation Trust, Manchester, United Kingdom., Nathrath M; Children's Cancer Research Center, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.; Pediatric Oncology, Klinikum Kassel, Kassel, Germany.

Publikováno v: Clinical cancer research : an official journal of the American Association for Cancer Research [Clin Cancer Res] 2024 Aug 15; Vol. 30 (16), pp. 3395-3406.

Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data.

Autor: Osorio D; Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA. daniecos@uio.no., Capasso A; Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA., Eckhardt SG; Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA., Giri U; Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA., Somma A; Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA., Pitts TM; Division of Medical Oncology, University of Colorado Cancer Center, School of Medicine, University of Colorado, Aurora, CO, USA., Lieu CH; Division of Medical Oncology, University of Colorado Cancer Center, School of Medicine, University of Colorado, Aurora, CO, USA., Messersmith WA; Division of Medical Oncology, University of Colorado Cancer Center, School of Medicine, University of Colorado, Aurora, CO, USA., Bagby SM; Division of Medical Oncology, University of Colorado Cancer Center, School of Medicine, University of Colorado, Aurora, CO, USA., Singh H; Department of Immunology, Center for Systems Immunology, University of Pittsburg, Pittsburg, PA, USA., Das J; Department of Immunology, Center for Systems Immunology, University of Pittsburg, Pittsburg, PA, USA., Sahni N; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.; Department of Bioinformatics and Computational Biology, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA., Yi SS; Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA. stephen.yi@austin.utexas.edu.; Interdisciplinary Life Sciences Graduate Programs (ILSGP), College of Natural Sciences, The University of Texas at Austin, Austin, TX, USA. stephen.yi@austin.utexas.edu.; Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, USA. stephen.yi@austin.utexas.edu.; Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, USA. stephen.yi@austin.utexas.edu., Kuijjer ML; Centre for Molecular Medicine Norway (NCMM), University of Oslo, Oslo, Norway. marieke.kuijjer@ncmm.uio.no.; Department of Pathology, Leiden University Medical Center (LUMC), Leiden University, Leiden, The Netherlands. marieke.kuijjer@ncmm.uio.no.; Leiden Center for Computational Oncology, Leiden University Medical Center (LUMC), Leiden University, Leiden, The Netherlands. marieke.kuijjer@ncmm.uio.no.

Publikováno v: Nature computational science [Nat Comput Sci] 2024 Mar; Vol. 4 (3), pp. 237-250. Date of Electronic Publication: 2024 Mar 04.

Single-sample network modeling on omics data.

Autor: De Marzio M; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medicine School, Boston, MA, USA., Glass K; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medicine School, Boston, MA, USA. kimberly.glass@channing.harvard.edu.; Biostatistics Department, Harvard Chan School of Public Health, Boston, MA, USA. kimberly.glass@channing.harvard.edu., Kuijjer ML; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway. marieke.kuijjer@ncmm.uio.no.

Publikováno v: BMC biology [BMC Biol] 2023 Dec 29; Vol. 21 (1), pp. 296. Date of Electronic Publication: 2023 Dec 29.

Heterogeneity in the gene regulatory landscape of leiomyosarcoma.

Autor: Belova T; Computational Biology and Systems Medicine Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway., Biondi N; Precision Sarcoma Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases, Heidelberg, Germany., Hsieh PH; Computational Biology and Systems Medicine Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway., Lutsik P; Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.; Department of Oncology, Catholic University (KU) Leuven, Leuven, Belgium., Chudasama P; Precision Sarcoma Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases, Heidelberg, Germany., Kuijjer ML; Computational Biology and Systems Medicine Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway.; Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands.; Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, the Netherlands.

Publikováno v: NAR cancer [NAR Cancer] 2023 Jul 24; Vol. 5 (3), pp. zcad037. Date of Electronic Publication: 2023 Jul 24 (Print Publication: 2023).